<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>The file is generated any time you provide GFF3 input. It is just a quick way to pull out the features for a region via SQLite. It's generated at the start of a MAKER run.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> <<a href="mailto:Sean.Li@csiro.au">Sean.Li@csiro.au</a>><br><span style="font-weight:bold">Date: </span> Wednesday, 1 August, 2012 10:45 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>, <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> RE: [maker-devel] The est_gff option<br></div><div><br></div><div xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"><meta name="Generator" content="Microsoft Word 12 (filtered medium)"><style><!--
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</o:shapelayout></xml><![endif]--><div lang="EN-AU" link="blue" vlink="purple"><div class="WordSection1"><p class="MsoNormal"><span style="color:#1F497D">Dear Carson,<o:p></o:p></span></p><p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p><p class="MsoNormal"><span style="color:#1F497D">Thank you for your explanation! Now I understand how the RNA-Seq data’s been interpreted in MAKER. I check the tag est_gff and only found it in a binary db file: the scaffold_56.db, which should be a SQLite file. I guess this is right? Will this file be only generated when est data’s been provided or I turned the alt_splice to 1? As the db file didn’t exist for my first run of Maker when no EST flags have been switched on.<o:p></o:p></span></p><p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p><p class="MsoNormal"><span style="color:#1F497D">Best regards,<o:p></o:p></span></p><p class="MsoNormal"><span style="color:#1F497D">Sean <o:p></o:p></span></p><p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p><div><div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"><p class="MsoNormal"><b><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; ">From:</span></b><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; "> Carson Holt [<a href="mailto:carsonhh@gmail.com">mailto:carsonhh@gmail.com</a>] <br><b>Sent:</b> Thursday, 2 August 2012 11:40 AM<br><b>To:</b> Li, Sean (CMIS, Acton); <a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><br><b>Subject:</b> Re: [maker-devel] The est_gff option<o:p></o:p></span></p></div></div><p class="MsoNormal"><o:p> </o:p></p><div><p class="MsoNormal"><span style="font-size:10.5pt;color:black">The mRANseq reads from GFF3 don't need to be blasted/exonerate polished because they are already aligned (so no run.log entry is generated), they are just popped into an alignment object in memory and integrated directly. The run.log file is used primarily to track finished calls to external programs (I.e. to avoid partial results files on failure). So since there is nothing to run, there is no run.log entry. You will just get a message saying reading GFF3 in STDERR. The GFF3 results are combined with any other results produced within maker and are then used to generate hints for gene predictors you run as to the location of introns/exons. This is during the step where you see SNAP or augustus running again and again. They also become part of the AED score for selecting from the pool of gene models, and can be used to add UTR to resulting gene models. If you specify alt_splice=1 they can even be used to infer alternate splice forms. For reference purposes, they will end up in the maker results with the tag est_gff:Cufflinks.<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:10.5pt;color:black">Thanks,<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:10.5pt;color:black">Carson<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p></div><div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"><p class="MsoNormal"><b><span style="color:black">From: </span></b><span style="color:black"><<a href="mailto:Sean.Li@csiro.au">Sean.Li@csiro.au</a>><br><b>Date: </b>Wednesday, 1 August, 2012 9:21 PM<br><b>To: </b><<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><b>Subject: </b>[maker-devel] The est_gff option<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p></div><div><div><p class="MsoNormal"><span style="color:black">Hello,<o:p></o:p></span></p><p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p><p class="MsoNormal"><span style="color:black">We are trying to add RNA-Seq data into the Maker run. As they have been properly aligned to our draft scaffolds by Cufflinks, we just gave the appropriate gff file to the est_gff option. The gff file is with the following format:<o:p></o:p></span></p><p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p><p class="MsoNormal"><span style="color:black">….<o:p></o:p></span></p><p class="MsoNormal"><span style="color:black">scaffold_56 Cufflinks match_part 248833 249471 . + . ID=1:TCONS_00039698:exon-1;Name=1:TCONS_00039698;Parent=1:TCONS_00039698;Target=1:TCONS_00039698 121525597 121526235 +;<o:p></o:p></span></p><p class="MsoNormal"><span style="color:black">scaffold_56 Cufflinks match_part 253262 253362 . + . ID=1:TCONS_00039698:exon-2;Name=1:TCONS_00039698;Parent=1:TCONS_00039698;Target=1:TCONS_00039698 121526236 121526336 +; <o:p></o:p></span></p><p class="MsoNormal"><span style="color:black">….<o:p></o:p></span></p><p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p><p class="MsoNormal"><span style="color:black">All the prediction algorithms have been trained before running Maker. Meanwhile, we provided the protein homology evidence. By simply checking the run.log file, I couldn’t find any records that show how RNA-Seq got involved into the prediction process (no blastn or exonerate for est). Is there anything I missed so the RNA-Seq evidence didn’t include in the prediction? Do I need to turn the est2genome on, since I suspect this option is only used when the algorithms aren’t trained properly? Or, do we need to set the value of pcov_blastn and eval_blastn a bit lower?<o:p></o:p></span></p><p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p><p class="MsoNormal"><span style="color:black">Thanks! <o:p></o:p></span></p><p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p><p class="MsoNormal"><span style="color:black">Regards,<o:p></o:p></span></p><p class="MsoNormal"><span style="color:black">Sean <o:p></o:p></span></p><p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p><p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p><p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p></div></div><p class="MsoNormal"><span style="font-size:10.5pt;color:black">_______________________________________________ maker-devel mailing list <a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a> <a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a> <o:p></o:p></span></p></div></div></div></span></body></html>